* using log directory 'd:/RCompile/CRANincoming/R-devel/ApplyPolygenicScore.Rcheck'
* using R Under development (unstable) (2024-07-25 r86925 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ApplyPolygenicScore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ApplyPolygenicScore' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Paul Boutros <PBoutros@mednet.ucla.edu>'

New submission

Possibly misspelled words in DESCRIPTION:
  Polygenic (3:43)
  SNP (12:5)
  SNPs (11:22)
  VCF (3:64, 10:40)
  genotype (10:5, 10:51)
  polygenic (11:42, 12:43)

Found the following (possibly) invalid URLs:
  URL: https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format
    From: README.md
    Status: 403
    Message: Forbidden
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ApplyPolygenicScore' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with invalid ORCID identifiers:
  Nicole Zeltser [aut] (000-0001-7246-2771)
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
merge:
  function(x, y, ...)
merge.pgs.bed:
  function(pgs.bed.list, add.annotation.data, annotation.column.index,
           slop)

merge:
  function(x, y, ...)
merge.vcf.with.pgs:
  function(vcf.data, pgs.weight.data)
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [36s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                                           user system elapsed
create.pgs.density.plot                   10.85   2.53   14.27
create.pgs.with.continuous.phenotype.plot  7.85   2.47   11.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [62s] OK
  Running 'testthat.R' [62s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s] OK
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 NOTEs